The document provides an overview of J&J's grid computing project including: 1) The goals of the project were to enable new ways of doing science by providing adequate computing capacity at reasonable cost, speed up the scientific process, and lower costs. 2) Applications included molecular docking, pharmacokinetic modeling, pharmacophore searching, and molecular force field calculations. 3) The grid evolved from 2004 pilots to a production environment in 2006 supporting over 1,200 CPUs and 15 production applications.

1. BE Grid Seminar
Information Technology
SLT Update
June 12th 2007
J&J, Medicines & Neutricionals IT
Serge Masyn
12 Jun 2007

2. BE Grid Seminar
Acknowledgements
• Information Technology
– Jeffrey Mathers, Director Pharma R&D IT - Research & Innovation
– Patrick Marichal, RED IT Program Manager
– David Neilson, Senior Director Global RED IT, now CIO ALZA
• Business
– Senior Business Sponsorship
– Trevor Howe, Wendy Sanderson, Pascal Bonnet, …Scientists
Molecular Informatics
– Andrew Chow, Don Heald, …Scientists Clinical Pharmacology
– Scientists and IT staff who voluntarily put their PC in the GRID
• Supplier
– The United Devices Project Lead and Team
12 Jun 2007

3. BE Grid Seminar
Johnson & Johnson Background
• 190+ Operating Companies
– Ortho McNeil, Janssen Pharmaceutica, Tibotec, DePuy, …
• 100K+ Employees
• Organized into Consumer, MD&D, Medicines & Neutricionals Sectors
• More than a thousand products in more than hundred categories
– Neutrogena , Piz Buin , Acuvue , Benecol , Listerine, …
TM TM TM TM
– Prezista , Motilium , Imodium , Risperdal , Duragesic , …
TM TM TM TM TM
– OneTouch , Knee Transplants, Surgery Kits,
TM
• Decentralized Management System
• Globally Diverse
• Constant State of Change
• Value based culture: Our Credo
12 Jun 2007

4. BE Grid Seminar
Major R&D Sites
~10,000 HC
TRANSFORM, Boston
J&J PRD, Beerse
ALZA, MT View
J&J PRD, La Jolla
TIBOTEC
J&J PRD, Spring House
CENTOCOR
J&J PRD, Titusville
J&J PRD, Raritan
Major R&D SITES
(##) Approx Headcount YE 2006
18 December 2003
12 Jun 2007

5. BE Grid Seminar
Janssen Pharmaceutica & J&J PRD background
Janssen Pharmaceutica, Beerse,
Belgium
Dr. Paul Janssen created
Janssen Pharmaceutica in 1953
Part of Johnson & Johnson
since 1961
Invented over 75 new drugs
Dr. Paul Janssen Research Center
Inaugurated in 2004
~10 000 employees
12 Jun 2007

6. BE Grid Seminar
The Grid Project - Business Drivers
• Increasing pressure to shorten cycle times for drug
development
– 12-15 years from inception to market
• Continual pressure to reduce drug development costs
– Mio $1,000+
• Continual pressure to
– Increase return on investment
– Provide added value
– Reduce the cost of ownership of
information technology
12 Jun 2007

7. BE Grid Seminar
Challenges & Opportunities
• Data explosion requiring more
computing intensive platforms
• Increased complexity and use of
in-silico models requiring
computing intensive platforms
• High investment & maintenance
cost of high performance
computing platforms
• Faster desktops at our availability
• Untapped potential
of cycle times of
fast desktops at
our disposal
12 Jun 2007

8. BE Grid Seminar
The Evolution of the Grid at J&J
2004 2006
Ran pilots with different suppliers with ARDA Service Model in 2006
moderate success
Pilot Project with United Devices in 2004 Production Environment
1 United Devices Meta-Platform Server United Devices 5.1/ MP Insight 3.2 (Go
running 300 concurrent licenses Live: 20-Dec-2004)
In total 376 Nodes or 420 CPU’s Currently 1200 CPUs (60/40 Win/Lin)
Early Adopters Users 35 Registered users
2 primary users 8 “hard core” users
2 (pilot) applications 15 production applications,
Virtual Screening Project 5 “hard core” apps
PK modelling project
VS core job processed 2005 processed 18,000 jobs
Consumed 22735 cpu hrs = 939 cpu days 20K GHz hrs/month – sometimes more
Limited startup cost IAR order of maintenance cost of High
Performance platforms; yearly 10% of
IAR maintenance fee
12 Jun 2007

9. BE Grid Seminar
J&J PRD’s Grid Definition
A collection of networked computer resources managed by
one or more software agents that is made to resemble in
use and in measure, a less granular computational
resource. Typical Grid Use Case
12 Jun 2007

10. BE Grid Seminar
The Distributed (Grid) Computing Project Goals
• Enable new ways of doing science
– By providing adequate computing capacity at reasonable cost allowing to
introduce new algorithms and tools
• Speed up the scientific process
– By boosting calculation time
– By better targeting physical screening campaigns
• Enable Data Driven Decision Making
– By applying in-silico models and predictive tools
• Lower the cost
– Of physical screening campaigns by better targeting
– By better usage of the global available capacity of high performance
computing infrastructure
– By better usage of the desktop computing infrastructure
12 Jun 2007

11. BE Grid Seminar
PhRD Example: Receptor-Ligand Docking
•Identify best candidate
families for physical screening
•Identify candidates that we
do not have in physical
inventory
•Reduction in synthesis
time/cost; screening
time/cost
Stereo view of benzamidine (red) docked in the active site of trypsin (blue) (PDB structure ID 3ptb), source http://cnx.org/
12 Jun 2007

12. BE Grid Seminar
PhRD Example: Pharmacophore Based Screening
Test1:
3D FlexSearch of the commercial available database (234 056
cpds)
Query includes the following features:
- H-Bond donors and acceptors, hydrophobic groups, partial match,
Markush formula
And the following constraints:
- surface volume, spatial points, spatial plane, torus
Test2:
3D FlexSearch of an in-house database ( ~3.3 millions cpds)
Query includes the following features:
- H-Bond donor, 2 hydrophobics with spatial point constraints
Test1 Test2
Devices CPU Job time (h) CPU Job time (h)
SGI O200 4 X Mips R12000, 360 MHz 30h 34 min.
SGI Fuel 1 X Mips R14000, 600 MHz 86h 02 min. 1 X Mips R14000, 600 MHz XX
Intel / Linux 1 X Intel Xeon, 3.6 GHz 55h 1 X Intel Xeon, 3.6 GHz ~100 days
GRID (hitlist) 360 connected devices (avg) 2h 42 min
GRID (Unity DB) 360 connected devices (avg) 1h 45 min 262 connected devices (avg) ~17h
12 Jun 2007

13. BE Grid Seminar
PhRD Example: PK Dose Modeling
• Parallel Model Optimization
• Rigorous model testing
• Automated Optimization
• Benefits:
– 20-40% reduction in model
optimization time
– ~10-15% higher quality
models
• Key projects: series of must-
do compounds in drug
development pipeline
PK, pharmacokinetics, what does the body to the drug
12 Jun 2007

14. BE Grid Seminar
Today’s Application Base
• Molecular Informatics
– Protein-Ligand Docking
– Pharmacokinetic Modelling and Trial Simulation
– Pharmacophore Search
– Molecular Mechanical Force Fields Calculations for the simulation of
Biomolecules
• Genomics-Bioinformatics
– BLAST 2.0, (Basic Local Alignment Search Tool), provides a method for
rapid searching of nucleotide and protein databases.
– Gene Expression Micro Array Analysis
• Potential Applications
– Image Rendering
– Sales & Marketing Data Mining
– Accelerating Natural Language Processing
– SAS-integration
– Mathematica Integration
12 Jun 2007

15. BE Grid Seminar
From Skunk works Pilot to Service Model
Program Delivery
United Devices Technical Support Management/Monitoring
In House Technical Expertise Capacity Scaling
Software Infrastructure
Hardware Infrastructure
12 Jun 2007

16. BE Grid Seminar
The Grid Community
12 Jun 2007

17. BE Grid Seminar
Grid Reward and Recognitions
• The Grid project has been awarded externally and
internally for its innovation in IT, having transformed
businesses processes, and for creating unprecedented
opportunities.
– UD Vision Award, 2006
– J&J EUIM Best poster, 2005
– Data News ICT Manager of the Year Award, 2005
– J&J Corporate IMAGE Award, 2005
– J&J Standards of Leadership Awards, 2003-2006
– More to be announced…
12 Jun 2007